Eu recebi uma resposta para essa pergunta em um comentário no meu blog por Leonard Rosenthol da Adobe. A parte central de sua resposta é:
The native content is stored in a special location in the PDF (see PieceInfo, ISO 32000-1:2008, 14.5) it does NOT create an embedded file.
Why? Two reasons – 1) Illustrator was doing this long before PDF supported attachments and 2) We don’t want users extracting out the private info.